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Following the highs and lows of a new PhD student making her way in the world of organic chemistry...

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As the weather finally begins to pick up and the remaining undergraduates frolick down by the lake in post-exam bliss, us postgrads take up our traditional "staring out of the tinted lab window and sighing quietly" routine...



It's a bank holiday this weekend, and The Boss ("we're not a bank") seems to think we'll all be working on Monday, but I reckon a few hours in the sunshine is nourishing for the body and soul. Enjoy the mini-break everyone!

I'll be back on Tuesday, refreshed and ready to face whatever my chemistry throws at me... 



(with thanks to bitstrips!)

Posted by Polly-Anna Ashford on May 25, 2013 2:33 PM GMT
Valentine's Day normally passes me by completely, but this year a charming young man in the lab next door decided to lift all our spirits by handing out beautiful red roses. 

Not being the cute and fluffy type, I stuck my thorny gift in a bottle of water, placed it next to an old rotorvap bath and promptly forgot about it. By the end of the day somebody had reminded me it was there (by taking the proverbial, as is tradition in the lab) and I examined it for signs of solvent abuse. 

The poor flower was in a sorry state. The petals had darkened and gone limp, in fact the entire head of the rose, unable to fight gravity in its flaccid state, was drooping mournfully into the bench. I shrugged, made a mental note not to work in a lab for too many years and went home expecting to find a rotting mess the next morning. 

Not so fast! In fact my charge had perked up quite considerably by the next day as you can see in the picture; it was in danger of looking almost healthy. The only explanation I can think of for this is that the lab at night is a rather different place from the lab during the day. Lids stay on solvent bottles and the fumehood vents aren't disturbed by herds of marauding project students so they very efficiently expel nasties from the room.

I was rather impressed so I fed it some alpha-D-glucose, the only bottle of sugar on my bench. The spatula wasn't clean so I hope it didn't mind absorbing some diazo compound as well. M'colleague left a couple of bits of dry ice underneath it for the CO2 hit and it seems to be thriving! Nice to cheer the place up every now and then. I'll let you know how long it lasts...

Maybe the lab atmosphere isn't as poisonous as I tend to imagine...
Posted by Polly-Anna Ashford on Feb 15, 2013 10:25 PM GMT


I'm sitting at a large table in a small room. The Boss waves a hand in my direction and I rise, taking a green whiteboard marker from the previous victim. 
I'm not terribly nervous. I've been off sick for a few days, and I've been doing repeat reactions, nothing new, nothing unfamiliar. 

And anyway, I'm a third year PhD, I know this stuff like the back of my hand. 

I write out the first reaction. Acid, alcohol, DCC, DMAP. 

"Sorry, what's DCC?" Pipes up an undergraduate. 

I open my mouth to answer. 

"It's a coupling reagent. Dicyclohexyl..." I trail off as the entire contents of my brain vanishes in a puff of smoke. 

Dicyclohexyl what? This is ridiculous, I've written the mechanism out at least 5 times. Why can't I remember the name of the reagent?!

A French masters student saves me and I feel the hot burn of humiliation.                                                                                                     
Moving swiftly on I try to recover and draw out the second route. Except I can't remember it. Not the starting materials or the reagents, even the product. This is silly, I've done this chemistry a hundred times! My pen hovers an inch from the board. I can't turn round, just imaging their faces is bad enough. No one speaks. 

I grope around in my head and it has never seemed so empty. I cant think, nothing is firing! Panic sets in but I manage apply some logic. 

Diazo compounds, therefore usually something to do with tosyl hydrazine. Ditosylhydrazine!! The rest follows and I breathe a sigh of relief. 

As I sit down a headache kicks in. 

That has never happened to me before. It was pretty scary. It was like forgetting to eat lunch or stop at a red light. Stress? Tiredness? No idea. I really hope it never happens again. Especially not in my viva.

Posted by Polly-Anna Ashford on Feb 11, 2013 1:19 PM GMT
As the year draws to a close, and I realise I haven’t blogged for 3 months, it’s time for a round up of all the fun and nonsense in (and out) of the lab in the past year.

Fluorochem surprised me with a free t-shirt for the summer, very trendy don’t ya think? And in the lab, it became clear that a thorough defrosting was necessary to remove the very bizarre ice sculptures...

      

The Boss continues to leave little notes on my bench when he misses me, and Herman the German friendship cake took the Chemistry department by storm, giving me my Mary Berry moment.

     

Exciting news: more...
Posted by Polly-Anna Ashford on Dec 30, 2012 8:44 PM GMT
The Genevac is basically a magic box.

You take your nasty solvent-binding novel compounds (of which you must get clean NMR spectra, or the world will end), put them in tiny glass vials, pop them inside the magic box and lock the door. Several hours later, your compounds are drier than a nun’s knickers handful of the Sahara desert.

Alright, this thing isn’t quite The TARDIS. It just spins the vials very fast under a high vacuum. And we love it.
Disaster struck a few months ago, when our magic box stopped being magic. General panic ensued, and after three hours in the instrument room with a toolbox and half a litre of silicon oil, our resident expert1 emerged with the verdict.

The pump was dead.

Cut to a few weeks later, and I was sitting by the harbour of a small fishing village in West Dorset when I got the text message...

“How far are you from Tintagel?”


more...
Posted by Polly-Anna Ashford on Sep 26, 2012 9:23 PM GMT
Approaching my third year, I feel much like I did when I was a teenager; desperate to leave home, live my own life, cook my own dinner and generally make my own decisions. In terms of chemistry, this means that I’m able to work independently in the lab, I’ve got plenty of ideas that I’d love to try out and I have my own clear plan for my project, but I’m under someone else’s roof, so I have to play by their rules. 



I’m not trying to say that any one approach is correct. There are many. Perhaps it’s only fair that we do as we are told, after all it’s the supervisor’s ideas and grant proposals and plain existence that allow us to be there in the first place. Are we not, as his group, simply the hands that put his ideas into practise? And if we have ideas of our own, well, there’s always the weekend...

Group leaders, I sympathise, I really do. I know that you work hard and that the job can be stressful and tiring. I know that supervising students is frustrating when you only get half the story. I know that when it comes to a choice between finishing off a big paper and reading a 350 page thesis for your student, there’s a clear winner. I also know that many of you embrace the student-supervisor relationship and pour into it your support, energy and enthusiasm. I have seen brilliant PhD students being taken out for dinner by their supervisory team on graduation, and champagne corks popping for published papers.  I have also seen a student falling apart from exhaustion, having not eaten or slept properly for days, pushed for the sake of a deadline that was never going to be met.  

Zen teaches that the “worst” in life can be the most valuable because it has the most lessons to teach. That’s only true if we allow ourselves to learn. I’m trying to put this into practise with my summer student. I let her know when she’s doing something well and that I’ve noticed when she’s particularly skilful in the lab (her columns rock). I try to sound positive and be helpful, even when I’m actually in a horrific mood. I want her to feel that she’s making progress and learning. I’m firm when she makes the same mistake twice, but not angry.  I really want her to enjoy the experience of working in a research lab, the way I did when I started. And I want to prove to myself that the carrot really can be more valuable than the stick.

Posted by Polly-Anna Ashford on Aug 15, 2012 8:31 PM GMT
Some of you may know that my Other Passion (aside from organic synthesis) is classical equitation, which is basically horseriding but with fancy dressage moves on rather well bred Portugese horses. This recently resulted in me being booted off a highly-strung Lusitano gelding in the middle of a canter pirouette and making a right mess of my collarbone. It broke in three places, and I had to wait a few days for the right surgeon, so they finally got round to fixing it last week. I have a shiny new £500 titanium plate and a few screws holding all the bits together. The whole hospital experience was rather grim, but I’ll rant about that somewhere else. The question is, what happens next?




The drawback with organic chemistry is that (unlike dressage) you need two hands to do it. One of mine is in a sling for the next three weeks and needs another two weeks of rest after that plus a raft of physio before I can really use it. At the moment I can’t actually lift it. It will be a while before I have the energy and lack of pain required for a full day at work anyway, and since I can’t cycle/drive and there’s no bus, I’ll have to walk to uni every day. Walking hurts.  I’m in the second year of my PhD, and I have some decent results so it isn’t a total disaster, but what can I actually occupy myself with for the next month?

My initial thought, which echoed the Head of Department’s, was that it would be a great chance to write some thesis, particularly the introduction and experimental so far. A load of reading would also be really useful. I can type with my left hand ok, although a bit slowly, so it’s possible. But this does not directly benefit my supervisor. He has essentially lost one of his lab slaves worker bees which means reduced output for papers. The only way I can be useful to him is to write a publishable review, which coincidentally I’ve already done (see January’s Chem Soc Rev). So whose priorities are more important? Am I his worker or is he my PhD supervisor? Thesis or review? Or both?

I'm catching up with him on Tuesday to find out...
Posted by Polly-Anna Ashford on May 25, 2012 7:51 PM GMT
In a group of strangers, it will take just minutes (or even seconds) for the most out-going personalities to make themselves known. If, by chance, it’s a quiet group, I’m in my element. I can put forth my ideas and opinions easily and even enjoy asserting myself. When there are two or three people vying for the limelight however, I could fight for my space, but then the doubts creep in...

Is it worth it? What if I just say something stupid and embarrass myself? Everyone else seems to be better at this than me anyway, so there’s no point contributing.

The rational part of my brain is telling me that this is all wrong, that I’m there for a reason, everyone else is probably blagging it a bit anyway, and of course my opinions are just as valid as theirs. And yet I keep quiet and wait a turn that might never come.

This doesn’t just happen at work though; I do it in casual conversations too. An idea pops into my head, and there’s a convenient pause in the conversation for me to say something. I almost do, but then... I don’t. The thought process that controls this is so subconscious and so fast that I don’t even know why I chose not to speak. By that point it’s too late, and anyway it doesn’t matter, it was probably superfluous or mundane. Or, more tediously, maybe it was a question that I suddenly feel unsure about asking and hold back. Whatever it is, it’s easier to choose silence. Sometimes the conversation carries on in my head, my mind babbles away to itself and then I realise I’ve been quiet for far too long. My friend says she can tell when this is happening, my face must give me away!

Without sounding like a complete nutcase, I’m writing this blog entry to muse on WHY. Is it a lack of confidence? Plain old (PhD-induced) world-weariness? Does it stem from being an only child and happy in my own company? Ultimately (combined with a natural aptitude for quiet) I think the problem comes from experiential learning. When you get something right, you need to repeat it to make it stick.  Get shot down once, and it will stay with you for far longer.

What I need is someone to bring that confidence out, to reward the tentative steps towards getting my thoughts heard. But I’m not a little girl in a classroom any more. The unfortunate reality is this: if I don’t push myself, no one else will.
Posted by Polly-Anna Ashford on Apr 26, 2012 10:40 PM GMT
I was asked the inevitable question again the other evening... It pops up in every first conversation with a stranger.

‘I’m doing a PhD in Chemistry.’

I pause, waiting for The Reaction. I have only ever met one person who didn’t pull some sort of face at this point, and it turned out he was a retired hospital lab manager who knew a thing or two about biochemistry. In other words, he was One of Us. To the non-scientist, the concept of a chemistry PhD elicits several different responses simultaneously. The processing of these thoughts is the cause of The Face. I believe it comes down to a combination of the following:

     The PhD – The recent boom in undergraduate education means that many people of my generation have a first degree, but go back a generation or two and it’s less common. The number of people with PhDs is comparatively miniscule, and the chance of me coming across one outside the university is low. So, not only are they faced with someone who has been through higher education once already, but this crazy cat came back for more. This is seen as a) admirable and/or b) a bit weird.

     Chemistry. Physics = Professor Brian Cox, Chemistry = radioactive waste, oil spills, industrial leaks, bombs and drugs, depending on the interests and awareness of the non-scientist. This is seen as either a) cool or b) scary (more likely). By this point, you’ve been placed in one of two categories:

1)      Super clever scientist who does cool research into chemistry in order to cure cancer and save the world.
2)      Serious science geek. Wouldn’t know Michelangelo from Mozart.

The direction of conversation now depends entirely on the curiosity of the non-scientist. The scientist has no choice but to wait for one of two responses:

1)      So what is your research focussing on? (NB: comes with a swift caveat, “I probably won’t understand, will I?”)
2)      An awkward silence while everyone sips their drinks and tries to think of something to say.

I have this down to a fine art now, thanks to a Christmas party where I had to go through it with each of the 20 guests in turn. This is the working title of my PhD thesis:

“Studies towards the synthesis of novel vancomycin analogues via an organocatalytic aziridination methodology”

And here’s how I explain that: “You’ll have heard of MRSA... (pause for response – if they haven’t, and look like a Daily Mail reader, I go with “hospital superbug”) ... I’m making new antibiotics to cure it.”

In chemistry terms, that’s about a million miles from the truth, but it gives people a way in. There’s no need for a “well you won’t understand anyway” attitude. I’ll leave you with this conversation overheard in the girls toilets of the Student Union pub last week:

Girl A: Has Tom submitted his thesis?
Girl B: Nah, don’t fink so, he just left.
Girl A: You know, that really pisses me off, cos right, his degree was basically funded by tax-payers, yeah, so the public pay you to do the research, and then your thesis is like your way of giving them somefink back, right?
Girl B: Yeah, totally.
Girl A: Tosser.

Well said.
Posted by Polly-Anna Ashford on Apr 1, 2012 9:16 PM GMT
My first lab coat was a thing of beauty; 100% cotton, nice and thick (perfect for a cold lab) and it actually fitted quite nicely. It was my school lab coat, though it would have done a very good job in a research lab too. Unfortunately when I was 17 I spilled something on it (not sure what, but I suspect permanganate was involved) and my mother, bless her, put it in the washing machine. It came out looking like the victim of a colony of clothes moths.

My second lab coat was supplied by the university, on my very first day as an undergraduate in the teaching laboratory. It was a polyester/cotton mix (ugh) and it was quite thin. It was also quite large, because I was quite large back then too. Within two years I had dropped nearly 3 dress sizes and I could have used it as a tent. By then I was working in my current lab in my spare time, and there was a pile of unwanted coats in the corner, so I grabbed the smallest one I could find and wrote my name on the label in permanent marker.

During a particularly hot summer, it sat on the hook unloved for a while (don’t tell on me) and unfortunately became hideously contaminated by a visiting student with a body odour problem who left his coat snuggling up to mine every day. I triple bagged it, took it home and gave it a thorough wash/decontamination/24 hours in a sheep dip.

It is clean now, which is its only redeeming feature. I’ve always hated wearing a lab coat. Not because I think it’s silly or unnecessary but because it’s uncomfortable and a nuisance. Part of the problem is that lab coats are so generic. They come in XS, S, M, L, XL. And that’s it. I am approximately a size “S” but the coat reaches below my knee, which is far too long and gets in the way, and I have to fold the sleeves to make them 3” shorter. Although an “S” fits my hips, it drowns my shoulders. “XS” fits my shoulders, but I can’t do it up further down.

You may think that I’m just whining about something trivial and unimportant, but I have to wear this bloody thing for at least 8 hours a day. Why should it be a chore? Just because it’s for safety doesn’t mean it has to be irritating. So  if anyone has any ideas about where I can get a cotton lab coat designed for women, that comes in different lengths, please let me know. If not, I need to get hold of a sewing machine...
Posted by Polly-Anna Ashford on Mar 6, 2012 11:25 AM GMT
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